I agree the regular season champ getting the auto-bid makes for a truer and stronger 'champion' to rep the mid-major leagues. However, I would also worry about teams tanking in the conference tourneys which would greatly diminish play.

In keeping with the 'top half of conference' idea... a rule that teams must have a winning record in-conference in order to qualify for an at-large (similar to six-win bowl game requirement) would be an interesting option for the tournament/rules committees to discuss.

While we can debate quality of teams and tournament improvements ad nauseum, at the end of the day its always about money. Simply put, the NCAA sees more potential revenue from a 7th or 8th-place P5(P7) school than a 2nd-place mid-major.